\HeaderA{SpikeList-class}{Class "SpikeList" - Spike Intensity and Concentration List}{SpikeList.Rdash.class}
\aliasA{show,SpikeList-method}{SpikeList-class}{show,SpikeList.Rdash.method}
\keyword{classes}{SpikeList-class}
\begin{Description}\relax
A simple list-based class for storing red and green channel foreground and
background intensities, spot area and concentrations for external control spike on
spotted microarray.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("SpikeList", spike)} where spike
is a list. In the CALIB package, SpikeList objects are normally generated by function 
\code{\LinkA{read.spike}{read.spike}}.
\end{Section}
\begin{Section}{List Components}
Objects should contain the following list components:
\describe{ 
\item[\code{R}:] numeric matrix containing the red(Cy5) foreground intensities
of all external control spikes on arrays. Rows correspond to spikes and 
columns to arrays.

\item[\code{G}:] numeric matrix containing the green(Cy3) foreground intensities
of all external control spikes on arrays. 

\item[\code{Rb}:] numeric matrix containing the red(Cy5) background intensities
of all external control spikes on arrays. 

\item[\code{Gb}:] numeric matrix containing the green(Cy3) background intensities
of all external control spikes on arrays. 

\item[\code{RArea}:] numeric matrix containing the red(Cy5) spot areas of all 
external control spikes on arrays. 

\item[\code{GArea}:] numeric matrix containing the green(Cy3) spot areas of all 
external control spikes on arrays. 

\item[\code{RConc}:] numeric matrix containing the red(Cy5) known concentrations
of all external control spikes on arrays.

\item[\code{GConc}:] numeric matrix containing the green(Cy3) know concentrations
of all external control spikes on arrays.

\item[\code{genes}:] data.frame containing information on spikes spotted on the arrays.
Should include a character column Name containing names for all the spikes.
}
All of the matrices should have the same dimensions.
\end{Section}
\begin{Section}{Extends}
Class \code{"list"}, from data part.
Class \code{"vector"}, by class \code{"list"}.
\end{Section}
\begin{Section}{Methods}
This class inherits directly from class List, so any operation appropriate
for lists will work on objects of this class. In addition, SpikeList objects
can be \code{\LinkA{subsetted}{subsetted}}, \code{\LinkA{combined}{combined}}
and \code{\LinkA{merged}{merged}}. SpikeList objects will return dimensions and
hence functions such as \code{\LinkA{dim}{dim}}, \code{\LinkA{dimnames}{dimnames}},
\code{\LinkA{nrow}{nrow}} and \code{\LinkA{ncol}{ncol}} are defined.
Generic method \code{\LinkA{show}{show}} is applied on \code{SpikeList},
so SpikeList will print in a compact way.

SpikeList objects are used on functions such as \code{\LinkA{estimateParameter}{estimateParameter}} or on some
other data visualization functions like \code{\LinkA{plotSpikeHI}{plotSpikeHI}} in the CALIB package.
\end{Section}
\begin{Author}\relax
Hui Zhao
\end{Author}
\begin{References}\relax
the limma package
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{RGList\_CALIB}{RGList.Rul.CALIB}}.

\code{\LinkA{RGList}{RGList}} in limma package.
\end{SeeAlso}

